> On Tue, Aug 25, 2015 at 2:53 AM, Martina Devi <martinadevi2011.gmail.com>
> wrote:
>
> > Hello
> >
> > Despite adding the Na ions the charge is not integral.
>
>
> ​Adding Na ions would do nothing to solve a non-integer charge. Sodium
> ions have a net charge of +1, so there is no integer number of ions you can
> add to neutralize a non-integer charge :).
> ​
>
>
> > When I use a
> > standard base the whole system gets neutralizes. Is it due to the
> presence
> > of a non-standard base?
> >
>
> ​Yes, but the issue is a little more subtle than that.​ All nucleic acid
> residues have a net charge of -1... EXCEPT for terminal residues. All
> 3'-terminal RNA residues have a net charge of -0.6919 electrons (-0.6921
> for DNA), while all 5'-terminal RNA residues have a net charge of -0.3081
> electrons (-0.3079 for DNA). Since each strand needs both a 3'- and
> 5'-terminus, the net charge of a complete RNA or DNA strand is always an
> exact integer... which is good.
>
> But this can trip people up. If you make a custom 3'-terminal residue or
> custom 5'-terminal residue and constrain its charge to be an integer rather
> than the same as the charges I listed above, then when you pair it with a
> standard terminus on the other end, you will end up with a net charge of
> either -0.6919 (or 0.6921 for DNA) *or* -0.3081 (or -0.3079 for DNA) after
> you add "neutralizing" ions.
>
> This is exactly what happened to you -- your net charge after
> neutralization is -0.6919 (which tells me you are doing RNA). You will
> need to go back to your charge derivation for your custom 5'-terminal
> residue (which you called "OAU" per your latest email) and constrain the
> charge to be -0.3081 instead of 0 or -1.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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